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Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...
[jalview.git]
/
src
/
jalview
/
io
/
NewickFile.java
diff --git
a/src/jalview/io/NewickFile.java
b/src/jalview/io/NewickFile.java
index
b4f3a33
..
765ea95
100755
(executable)
--- a/
src/jalview/io/NewickFile.java
+++ b/
src/jalview/io/NewickFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-26,10
+26,14
@@
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.io.*;
-import java.util.StringTokenizer;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
@@
-106,7
+110,7
@@
public class NewickFile extends FileParse
*/
public NewickFile(String inStr) throws IOException
{
*/
public NewickFile(String inStr) throws IOException
{
- super(inStr, "Paste");
+ super(inStr, DataSourceType.PASTE);
}
/**
}
/**
@@
-114,15
+118,16
@@
public class NewickFile extends FileParse
*
* @param inFile
* DOCUMENT ME!
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param protocol
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public NewickFile(String inFile, String type) throws IOException
+ public NewickFile(String inFile, DataSourceType protocol)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, protocol);
}
public NewickFile(FileParse source) throws IOException
}
public NewickFile(FileParse source) throws IOException
@@
-295,7
+300,7
@@
public class NewickFile extends FileParse
int nextcp = 0;
int ncp = cp;
int nextcp = 0;
int ncp = cp;
- boolean parsednodename=false;
+ boolean parsednodename = false;
while (majorsyms.searchFrom(nf, cp) && (Error == null))
{
int fcp = majorsyms.matchedFrom();
while (majorsyms.searchFrom(nf, cp) && (Error == null))
{
int fcp = majorsyms.matchedFrom();
@@
-361,12
+366,13
@@
public class NewickFile extends FileParse
nodename = new String(qnodename.stringMatched().substring(1,
nl - 1));
// unpack any escaped colons
nodename = new String(qnodename.stringMatched().substring(1,
nl - 1));
// unpack any escaped colons
- com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex.perlCode("s/''/'/");
+ com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+ .perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
String widernodename = xpandquotes.replaceAll(nodename);
- nodename=widernodename;
+ nodename = widernodename;
// jump to after end of quoted nodename
nextcp = fcp + nl + 1;
// jump to after end of quoted nodename
nextcp = fcp + nl + 1;
- parsednodename=true;
+ parsednodename = true;
}
else
{
}
else
{
@@
-435,7
+441,8
@@
public class NewickFile extends FileParse
com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
":([-0-9Ee.+]+)");
com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
":([-0-9Ee.+]+)");
- if (!parsednodename && uqnodename.search(fstring)
+ if (!parsednodename
+ && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
@@
-594,7
+601,7
@@
public class NewickFile extends FileParse
distance = DefDistance;
bootstrap = DefBootstrap;
commentString2 = null;
distance = DefDistance;
bootstrap = DefBootstrap;
commentString2 = null;
- parsednodename=false;
+ parsednodename = false;
}
if (nextcp == 0)
{
}
if (nextcp == 0)
{
@@
-609,11
+616,14
@@
public class NewickFile extends FileParse
if (Error != null)
{
if (Error != null)
{
- throw (new IOException("NewickFile: " + Error + "\n"));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { Error.toString() })));
}
if (root == null)
{
}
if (root == null)
{
- throw (new IOException("NewickFile: No Tree read in\n"));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { MessageManager
+ .getString("label.no_tree_read_in") })));
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
@@
-957,7
+967,7
@@
public class NewickFile extends FileParse
treefile.close();
System.out.println("Read file :\n");
treefile.close();
System.out.println("Read file :\n");
- NewickFile trf = new NewickFile(args[0], "File");
+ NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
trf.parse();
System.out.println("Original file :\n");
trf.parse();
System.out.println("Original file :\n");